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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9039</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9040</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -163,7 +163,7 @@
<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">30 October 2022</h4>
<h4 data-toc-skip class="date">31 October 2022</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
<div class="d-none name"><code>AMR.Rmd</code></div>
@ -175,7 +175,7 @@ Berends</h4>
website update since they are based on randomly created values and the
page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
Markdown</a>. However, the methodology remains unchanged. This page was
generated on 30 October 2022.</p>
generated on 31 October 2022.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -231,21 +231,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2022-10-30</td>
<td align="center">2022-10-31</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2022-10-30</td>
<td align="center">2022-10-31</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2022-10-30</td>
<td align="center">2022-10-31</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -375,12 +375,12 @@ data set:</p>
<col width="13%">
<col width="13%">
<col width="13%">
<col width="26%">
<col width="28%">
<col width="5%">
<col width="5%">
<col width="5%">
<col width="5%">
<col width="9%">
<col width="8%">
</colgroup>
<thead><tr class="header">
<th align="center">date</th>
@ -395,68 +395,68 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2016-08-09</td>
<td align="center">B3</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">2012-05-31</td>
<td align="center">N10</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2017-05-13</td>
<td align="center">F3</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">2015-04-26</td>
<td align="center">I4</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2014-03-18</td>
<td align="center">N4</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">2016-07-16</td>
<td align="center">V10</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2011-05-13</td>
<td align="center">X4</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">2017-02-09</td>
<td align="center">W1</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2016-07-24</td>
<td align="center">R2</td>
<td align="center">Hospital D</td>
<td align="center">2016-09-11</td>
<td align="center">V5</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2010-11-05</td>
<td align="center">Q1</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">2010-08-24</td>
<td align="center">V1</td>
<td align="center">Hospital D</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
@ -494,16 +494,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,433</td>
<td align="right">52.17%</td>
<td align="right">10,433</td>
<td align="right">52.17%</td>
<td align="right">10,447</td>
<td align="right">52.24%</td>
<td align="right">10,447</td>
<td align="right">52.24%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,567</td>
<td align="right">47.84%</td>
<td align="right">9,553</td>
<td align="right">47.77%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -616,9 +616,9 @@ takes into account the antimicrobial susceptibility test results using
<span><span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
<span><span class="co"># 2</span></span>
<span><span class="co"># Including isolates from ICU.</span></span>
<span><span class="co"># =&gt; Found 10,691 'phenotype-based' first isolates (53.5% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,679 'phenotype-based' first isolates (53.4% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 53.5% is suitable for resistance analysis! We can now filter
<p>So only 53.4% is suitable for resistance analysis! We can now filter
on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the
<code>dplyr</code> package:</p>
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
@ -629,7 +629,7 @@ on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html"
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co"># Including isolates from ICU.</span></span></code></pre></div>
<p>So we end up with 10,691 isolates for analysis. Now our data looks
<p>So we end up with 10,679 isolates for analysis. Now our data looks
like:</p>
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></span></code></pre></div>
@ -669,78 +669,14 @@ like:</p>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2016-08-09</td>
<td align="center">B3</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="center">2017-05-13</td>
<td align="center">F3</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="center">2014-03-18</td>
<td align="center">N4</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="center">2011-05-13</td>
<td align="center">X4</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="center">2016-07-24</td>
<td align="center">R2</td>
<td align="center">Hospital D</td>
<td align="center">2012-05-31</td>
<td align="center">N10</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
@ -748,14 +684,30 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">8</td>
<td align="center">2011-10-07</td>
<td align="center">R2</td>
<td align="center">Hospital A</td>
<td align="left">5</td>
<td align="center">2016-09-11</td>
<td align="center">V5</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">7</td>
<td align="center">2012-07-11</td>
<td align="center">V1</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
@ -763,6 +715,54 @@ like:</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">8</td>
<td align="center">2017-09-04</td>
<td align="center">G4</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">10</td>
<td align="center">2010-08-06</td>
<td align="center">V2</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">14</td>
<td align="center">2012-06-25</td>
<td align="center">J2</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Time for the analysis!</p>
@ -796,8 +796,8 @@ readable:</p>
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 10,691<br>
Available: 10,691 (100%, NA: 0 = 0%)<br>
Length: 10,679<br>
Available: 10,679 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -822,33 +822,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,653</td>
<td align="right">43.52%</td>
<td align="right">4,653</td>
<td align="right">43.52%</td>
<td align="right">4,629</td>
<td align="right">43.35%</td>
<td align="right">4,629</td>
<td align="right">43.35%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,711</td>
<td align="right">25.36%</td>
<td align="right">7,364</td>
<td align="right">68.88%</td>
<td align="right">2,722</td>
<td align="right">25.49%</td>
<td align="right">7,351</td>
<td align="right">68.84%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,142</td>
<td align="right">20.04%</td>
<td align="right">9,506</td>
<td align="right">88.92%</td>
<td align="right">2,112</td>
<td align="right">19.78%</td>
<td align="right">9,463</td>
<td align="right">88.61%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,185</td>
<td align="right">11.08%</td>
<td align="right">10,691</td>
<td align="right">1,216</td>
<td align="right">11.39%</td>
<td align="right">10,679</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -869,14 +869,14 @@ antibiotic class they are in:</p>
<col width="9%">
<col width="9%">
<col width="9%">
<col width="11%">
<col width="10%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="6%">
<col width="11%">
<col width="11%">
<col width="12%">
<col width="9%">
<col width="5%">
</colgroup>
@ -897,23 +897,68 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2016-07-24</td>
<td align="center">R2</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">2012-07-11</td>
<td align="center">V1</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-10-07</td>
<td align="center">R2</td>
<td align="center">2010-11-11</td>
<td align="center">A2</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2015-04-22</td>
<td align="center">X9</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-04-02</td>
<td align="center">G5</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2017-04-01</td>
<td align="center">S1</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
@ -926,29 +971,14 @@ antibiotic class they are in:</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2016-06-18</td>
<td align="center">R8</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2015-09-18</td>
<td align="center">D3</td>
<td align="center">Hospital C</td>
<td align="center">2012-05-06</td>
<td align="center">D1</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
@ -956,36 +986,6 @@ antibiotic class they are in:</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2017-02-04</td>
<td align="center">Y10</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-11-13</td>
<td align="center">P2</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>If you want to get a quick glance of the number of isolates in
@ -1009,50 +1009,50 @@ different bug/drug combinations, you can use the
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2175</td>
<td align="center">152</td>
<td align="center">2326</td>
<td align="center">4653</td>
<td align="center">2177</td>
<td align="center">124</td>
<td align="center">2328</td>
<td align="center">4629</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3423</td>
<td align="center">161</td>
<td align="center">1069</td>
<td align="center">4653</td>
<td align="center">3412</td>
<td align="center">170</td>
<td align="center">1047</td>
<td align="center">4629</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3409</td>
<td align="center">3331</td>
<td align="center">0</td>
<td align="center">1244</td>
<td align="center">4653</td>
<td align="center">1298</td>
<td align="center">4629</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4080</td>
<td align="center">4046</td>
<td align="center">0</td>
<td align="center">573</td>
<td align="center">4653</td>
<td align="center">583</td>
<td align="center">4629</td>
</tr>
<tr class="odd">
<td align="center">K. pneumoniae</td>
<td align="center">AMX</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">1185</td>
<td align="center">1185</td>
<td align="center">1216</td>
<td align="center">1216</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">939</td>
<td align="center">39</td>
<td align="center">207</td>
<td align="center">1185</td>
<td align="center">943</td>
<td align="center">52</td>
<td align="center">221</td>
<td align="center">1216</td>
</tr>
</tbody>
</table>
@ -1075,34 +1075,34 @@ different bug/drug combinations, you can use the
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4080</td>
<td align="center">4046</td>
<td align="center">0</td>
<td align="center">573</td>
<td align="center">4653</td>
<td align="center">583</td>
<td align="center">4629</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1060</td>
<td align="center">1095</td>
<td align="center">0</td>
<td align="center">125</td>
<td align="center">1185</td>
<td align="center">121</td>
<td align="center">1216</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2400</td>
<td align="center">2420</td>
<td align="center">0</td>
<td align="center">311</td>
<td align="center">2711</td>
<td align="center">302</td>
<td align="center">2722</td>
</tr>
<tr class="even">
<td align="center">S. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">2142</td>
<td align="center">2142</td>
<td align="center">2112</td>
<td align="center">2112</td>
</tr>
</tbody>
</table>
@ -1134,7 +1134,7 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
own:</p>
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
<span><span class="co"># [1] 0.5446637</span></span></code></pre></div>
<span><span class="co"># [1] 0.549396</span></span></code></pre></div>
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and
<code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
@ -1149,19 +1149,19 @@ own:</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5453964</td>
<td align="center">0.5496112</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5342941</td>
<td align="center">0.5540966</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5604129</td>
<td align="center">0.5353956</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5495620</td>
<td align="center">0.5518987</td>
</tr>
</tbody>
</table>
@ -1186,23 +1186,23 @@ all isolates available for every group (i.e. values S, I or R):</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5453964</td>
<td align="center">3128</td>
<td align="center">0.5496112</td>
<td align="center">3215</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5342941</td>
<td align="center">3747</td>
<td align="center">0.5540966</td>
<td align="center">3808</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5604129</td>
<td align="center">1647</td>
<td align="center">0.5353956</td>
<td align="center">1681</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5495620</td>
<td align="center">2169</td>
<td align="center">0.5518987</td>
<td align="center">1975</td>
</tr>
</tbody>
</table>
@ -1227,27 +1227,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7702557</td>
<td align="center">0.8768536</td>
<td align="center">0.9735654</td>
<td align="center">0.7738172</td>
<td align="center">0.8740549</td>
<td align="center">0.9758047</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8253165</td>
<td align="center">0.8945148</td>
<td align="center">0.9839662</td>
<td align="center">0.8182566</td>
<td align="center">0.9004934</td>
<td align="center">0.9851974</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7941719</td>
<td align="center">0.8852822</td>
<td align="center">0.9793434</td>
<td align="center">0.7883909</td>
<td align="center">0.8890522</td>
<td align="center">0.9783248</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5359477</td>
<td align="center">0.5298295</td>
<td align="center">0.0000000</td>
<td align="center">0.5359477</td>
<td align="center">0.5298295</td>
</tr>
</tbody>
</table>
@ -1275,23 +1275,23 @@ classes, use a antibiotic class selector such as
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">54.5%</td>
<td align="right">26.7%</td>
<td align="right">55.0%</td>
<td align="right">27.0%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">53.4%</td>
<td align="right">26.2%</td>
<td align="right">55.4%</td>
<td align="right">25.8%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">56.0%</td>
<td align="right">27.6%</td>
<td align="right">53.5%</td>
<td align="right">25.3%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">55.0%</td>
<td align="right">25.7%</td>
<td align="right">55.2%</td>
<td align="right">28.5%</td>
</tr>
</tbody>
</table>
@ -1407,16 +1407,18 @@ classes) <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code>:</p>
<code class="sourceCode R"><span><span class="va">mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span>
<span><span class="va">mic_values</span></span>
<span><span class="co"># Class 'mic'</span></span>
<span><span class="co"># [1] 0.005 0.5 16 0.25 0.0625 128 0.025 0.01 0.005 0.125 </span></span>
<span><span class="co"># [11] 2 8 0.01 8 128 2 0.025 0.25 128 0.002 </span></span>
<span><span class="co"># [21] 0.001 0.25 0.025 0.001 1 32 0.25 &gt;=256 0.025 0.002 </span></span>
<span><span class="co"># [31] 32 0.025 2 4 0.125 128 8 0.25 2 4 </span></span>
<span><span class="co"># [41] 32 0.0625 8 4 0.125 8 0.125 0.025 16 0.01 </span></span>
<span><span class="co"># [51] 32 0.125 1 64 64 0.01 128 0.5 0.001 0.125 </span></span>
<span><span class="co"># [61] 32 4 0.005 0.001 0.005 0.002 0.5 0.01 0.25 2 </span></span>
<span><span class="co"># [71] &gt;=256 4 128 1 1 0.125 16 0.005 0.001 32 </span></span>
<span><span class="co"># [81] 128 0.5 0.0625 0.0625 32 0.002 4 0.025 0.0625 128 </span></span>
<span><span class="co"># [91] 4 2 2 &gt;=256 16 0.0625 &gt;=256 0.125 0.5 1</span></span></code></pre></div>
<span><span class="co"># [1] 64 16 0.01 0.01 32 1 0.25 2 &lt;=0.001</span></span>
<span><span class="co"># [10] 0.025 0.002 0.002 0.005 128 0.5 0.125 0.0625 4 </span></span>
<span><span class="co"># [19] 0.01 2 0.25 32 128 0.005 0.0625 0.005 0.01 </span></span>
<span><span class="co"># [28] 8 &lt;=0.001 0.002 &lt;=0.001 0.0625 &lt;=0.001 1 0.01 0.025 </span></span>
<span><span class="co"># [37] 0.0625 1 2 64 32 0.125 16 32 1 </span></span>
<span><span class="co"># [46] 16 8 0.002 4 0.0625 0.0625 4 0.01 0.0625 </span></span>
<span><span class="co"># [55] 0.25 0.0625 4 8 0.5 16 128 0.01 256 </span></span>
<span><span class="co"># [64] 1 8 32 0.002 2 2 4 8 8 </span></span>
<span><span class="co"># [73] 64 128 0.005 256 256 128 0.025 1 128 </span></span>
<span><span class="co"># [82] 0.01 0.002 0.5 0.002 0.5 0.002 2 &lt;=0.001 128 </span></span>
<span><span class="co"># [91] 256 0.005 8 0.125 256 64 0.025 32 0.002 </span></span>
<span><span class="co"># [100] 0.5</span></span></code></pre></div>
<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></span></code></pre></div>
@ -1450,10 +1452,10 @@ plotting:</p>
<code class="sourceCode R"><span><span class="va">disk_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_disk</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span>
<span><span class="va">disk_values</span></span>
<span><span class="co"># Class 'disk'</span></span>
<span><span class="co"># [1] 18 26 18 24 26 31 22 22 22 26 27 26 30 20 23 30 30 25 25 17 18 27 25 25 28</span></span>
<span><span class="co"># [26] 31 17 23 27 20 29 22 19 31 27 30 21 22 30 24 17 21 28 31 31 17 20 20 28 29</span></span>
<span><span class="co"># [51] 29 19 24 18 28 23 27 17 26 17 28 17 18 30 27 25 26 27 25 31 17 17 17 23 28</span></span>
<span><span class="co"># [76] 29 23 25 25 24 21 24 18 20 17 24 25 30 27 19 23 25 20 18 28 23 24 23 18 20</span></span></code></pre></div>
<span><span class="co"># [1] 25 24 24 22 25 22 25 30 24 19 19 31 19 19 26 22 23 30 25 30 21 26 31 21 23</span></span>
<span><span class="co"># [26] 21 27 22 17 22 25 18 28 25 17 28 25 22 30 29 27 24 20 24 28 24 19 21 26 25</span></span>
<span><span class="co"># [51] 21 19 31 21 26 21 25 26 18 20 24 24 19 23 18 25 28 27 30 29 21 29 19 31 19</span></span>
<span><span class="co"># [76] 21 17 29 28 26 20 29 29 26 27 30 19 21 23 28 19 21 25 31 17 20 26 20 19 29</span></span></code></pre></div>
<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></code></pre></div>

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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9039</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9040</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

56
articles/MDR.html
View File

@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9039</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9040</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -370,18 +370,18 @@ names or codes, this would have worked exactly the same way:</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
<span><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co"># 1 S S R R R R</span></span>
<span><span class="co"># 2 R I S R S S</span></span>
<span><span class="co"># 3 R I R S R I</span></span>
<span><span class="co"># 4 I R S I R I</span></span>
<span><span class="co"># 5 S S S R S S</span></span>
<span><span class="co"># 6 S I I R S I</span></span>
<span><span class="co"># 1 S S R S R I</span></span>
<span><span class="co"># 2 R R R I R R</span></span>
<span><span class="co"># 3 S S S S S R</span></span>
<span><span class="co"># 4 R R I R R I</span></span>
<span><span class="co"># 5 S R I S S S</span></span>
<span><span class="co"># 6 S I S S S I</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 R</span></span>
<span><span class="co"># 2 R</span></span>
<span><span class="co"># 1 I</span></span>
<span><span class="co"># 2 I</span></span>
<span><span class="co"># 3 I</span></span>
<span><span class="co"># 4 I</span></span>
<span><span class="co"># 5 I</span></span>
<span><span class="co"># 5 S</span></span>
<span><span class="co"># 6 R</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can
use:</p>
@ -423,40 +423,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3215</td>
<td align="right">64.30%</td>
<td align="right">3215</td>
<td align="right">64.30%</td>
<td align="right">3245</td>
<td align="right">64.90%</td>
<td align="right">3245</td>
<td align="right">64.90%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">1001</td>
<td align="right">20.02%</td>
<td align="right">4216</td>
<td align="right">84.32%</td>
<td align="right">989</td>
<td align="right">19.78%</td>
<td align="right">4234</td>
<td align="right">84.68%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">435</td>
<td align="right">8.70%</td>
<td align="right">4651</td>
<td align="right">93.02%</td>
<td align="right">415</td>
<td align="right">8.30%</td>
<td align="right">4649</td>
<td align="right">92.98%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">251</td>
<td align="right">5.02%</td>
<td align="right">4902</td>
<td align="right">98.04%</td>
<td align="right">247</td>
<td align="right">4.94%</td>
<td align="right">4896</td>
<td align="right">97.92%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">98</td>
<td align="right">1.96%</td>
<td align="right">104</td>
<td align="right">2.08%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

2
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9039</small>
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@ -38,7 +38,7 @@
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9039</small>
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@ -163,7 +163,7 @@
<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">30 October 2022</h4>
<h4 data-toc-skip class="date">31 October 2022</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
<div class="d-none name"><code>SPSS.Rmd</code></div>

2
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9039</small>
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9039</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9040</small>
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@ -161,7 +161,7 @@
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">30 October 2022</h4>
<h4 data-toc-skip class="date">31 October 2022</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="d-none name"><code>datasets.Rmd</code></div>
@ -191,7 +191,7 @@ column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</e
<em>gbif_renamed_to</em>, <em>prevalence</em> and <em>snomed</em>.</p>
<p>This data set is in R available as <code>microorganisms</code>, after
you load the <code>AMR</code> package.</p>
<p>It was last updated on 30 October 2022 20:06:52 UTC. Find more info
<p>It was last updated on 31 October 2022 10:20:17 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@ -490,7 +490,7 @@ column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>a
<em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p>
<p>This data set is in R available as <code>antibiotics</code>, after
you load the <code>AMR</code> package.</p>
<p>It was last updated on 30 October 2022 20:06:52 UTC. Find more info
<p>It was last updated on 31 October 2022 10:20:17 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@ -687,7 +687,7 @@ column names:<br><em>atc</em>, <em>cid</em>, <em>name</em>, <em>atc_group</em>,
<em>iv_ddd</em> and <em>iv_units</em>.</p>
<p>This data set is in R available as <code>antivirals</code>, after you
load the <code>AMR</code> package.</p>
<p>It was last updated on 30 October 2022 20:06:52 UTC. Find more info
<p>It was last updated on 31 October 2022 10:20:17 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@ -847,7 +847,7 @@ column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>
<em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
<p>This data set is in R available as <code>rsi_translation</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 30 October 2022 20:06:52 UTC. Find more info
<p>It was last updated on 31 October 2022 10:20:17 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@ -1020,7 +1020,7 @@ Resistance<a class="anchor" aria-label="anchor" href="#intrinsic_resistant-intri
column names:<br><em>mo</em> and <em>ab</em>.</p>
<p>This data set is in R available as <code>intrinsic_resistant</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 30 October 2022 20:06:52 UTC. Find more info
<p>It was last updated on 31 October 2022 10:20:17 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@ -1308,7 +1308,7 @@ column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>,
<em>original_txt</em> and <em>eucast_version</em>.</p>
<p>This data set is in R available as <code>dosage</code>, after you
load the <code>AMR</code> package.</p>
<p>It was last updated on 30 October 2022 20:06:52 UTC. Find more info
<p>It was last updated on 31 October 2022 10:20:17 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@ -1458,7 +1458,7 @@ column names:<br><em>date</em>, <em>patient</em>, <em>age</em>, <em>gender</em>,
<em>MUP</em> and <em>RIF</em>.</p>
<p>This data set is in R available as <code>example_isolates</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 30 October 2022 20:06:52 UTC. Find more info
<p>It was last updated on 31 October 2022 10:20:17 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates.html">here</a>.</p>
<div class="section level3">
<h3 id="source-6">Source<a class="anchor" aria-label="anchor" href="#source-6"></a>
@ -1871,7 +1871,7 @@ column names:<br><em>patient_id</em>, <em>hospital</em>, <em>date</em>,
<p>This data set is in R available as
<code>example_isolates_unclean</code>, after you load the
<code>AMR</code> package.</p>
<p>It was last updated on 30 October 2022 20:06:52 UTC. Find more info
<p>It was last updated on 31 October 2022 10:20:17 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates_unclean.html">here</a>.</p>
<div class="section level3">
<h3 id="source-7">Source<a class="anchor" aria-label="anchor" href="#source-7"></a>

2
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